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In this paper, a robot calibration method is proposed where the effects of joint compliance is taken into account when formulating the model. The calibration process identifies the parameters describing the relative poses of the local frames attached to the links of the robot and the parameters determining joint deflections such as joint stiffness, the mass and center of gravity of each link. A kinematic model of the robot which considers the effects of joint compliance is first formulated using the product-of-exponentials approach. Subsequently, the calibration process is described where the parameters within the robot model are updated based on measurement data. Finally, a comprehensive simulation study is conducted to validate the assumptions made during problem formulation and to verify the effectiveness of the proposed approach.